.TH g_sham 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_sham - read/write xmgr and xvgr data sets

.B VERSION 4.5
.SH SYNOPSIS
\f3g_sham\fP
.BI "\-f" " graph.xvg "
.BI "\-ge" " gibbs.xvg "
.BI "\-ene" " esham.xvg "
.BI "\-dist" " ener.xvg "
.BI "\-histo" " edist.xvg "
.BI "\-bin" " bindex.ndx "
.BI "\-lp" " prob.xpm "
.BI "\-ls" " gibbs.xpm "
.BI "\-lsh" " enthalpy.xpm "
.BI "\-lss" " entropy.xpm "
.BI "\-map" " map.xpm "
.BI "\-ls3" " gibbs3.pdb "
.BI "\-mdata" " mapdata.xvg "
.BI "\-g" " shamlog.log "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]time" ""
.BI "\-b" " real "
.BI "\-e" " real "
.BI "\-ttol" " real "
.BI "\-n" " int "
.BI "\-[no]d" ""
.BI "\-bw" " real "
.BI "\-[no]sham" ""
.BI "\-tsham" " real "
.BI "\-pmin" " real "
.BI "\-dim" " vector "
.BI "\-ngrid" " vector "
.BI "\-xmin" " vector "
.BI "\-xmax" " vector "
.BI "\-pmax" " real "
.BI "\-gmax" " real "
.BI "\-emin" " real "
.BI "\-emax" " real "
.BI "\-nlevels" " int "
.BI "\-mname" " string "
.SH DESCRIPTION
\&g_sham makes multi\-dimensional free\-energy, enthalpy and entropy plots.
\&g_sham reads one or more xvg files and analyzes data sets.
\&g_sham basic purpose is plotting Gibbs free energy landscapes
\&(option \fB \-ls\fR)
\&by Bolzmann inverting multi\-dimensional histograms (option \fB \-lp\fR)
\&but it can also
\&make enthalpy (option \fB \-lsh\fR) and entropy (option \fB \-lss\fR)
\&plots. The histograms can be made for any quantities the user supplies.
\&A line in the input file may start with a time
\&(see option \fB \-time\fR) and any number of y values may follow.
\&Multiple sets can also be
\&read when they are separated by & (option \fB \-n\fR),
\&in this case only one y value is read from each line.
\&All lines starting with  and @ are skipped.
\&


\&Option \fB \-ge\fR can be used to supply a file with free energies
\&when the ensemble is not a Boltzmann ensemble, but needs to be biased
\&by this free energy. One free energy value is required for each
\&(multi\-dimensional) data point in the \fB \-f\fR input.
\&


\&Option \fB \-ene\fR can be used to supply a file with energies.
\&These energies are used as a weighting function in the single
\&histogram analysis method due to Kumar et. al. When also temperatures
\&are supplied (as a second column in the file) an experimental
\&weighting scheme is applied. In addition the vales
\&are used for making enthalpy and entropy plots.
\&


\&With option \fB \-dim\fR dimensions can be gives for distances.
\&When a distance is 2\- or 3\-dimensional, the circumference or surface
\&sampled by two particles increases with increasing distance.
\&Depending on what one would like to show, one can choose to correct
\&the histogram and free\-energy for this volume effect.
\&The probability is normalized by r and r2 for a dimension of 2 and 3
\&respectively.
\&A value of \-1 is used to indicate an angle in degrees between two
\&vectors: a sin(angle) normalization will be applied.
\&Note that for angles between vectors the inner\-product or cosine
\&is the natural quantity to use, as it will produce bins of the same
\&volume.
.SH FILES
.BI "\-f" " graph.xvg" 
.B Input
 xvgr/xmgr file 

.BI "\-ge" " gibbs.xvg" 
.B Input, Opt.
 xvgr/xmgr file 

.BI "\-ene" " esham.xvg" 
.B Input, Opt.
 xvgr/xmgr file 

.BI "\-dist" " ener.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-histo" " edist.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-bin" " bindex.ndx" 
.B Output, Opt.
 Index file 

.BI "\-lp" " prob.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-ls" " gibbs.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-lsh" " enthalpy.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-lss" " entropy.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-map" " map.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-ls3" " gibbs3.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-mdata" " mapdata.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-g" " shamlog.log" 
.B Output, Opt.
 Log file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]time"  "yes   "
 Expect a time in the input

.BI "\-b"  " real" " \-1    " 
 First time to read from set

.BI "\-e"  " real" " \-1    " 
 Last time to read from set

.BI "\-ttol"  " real" " 0     " 
 Tolerance on time in appropriate units (usually ps)

.BI "\-n"  " int" " 1" 
 Read  sets separated by &

.BI "\-[no]d"  "no    "
 Use the derivative

.BI "\-bw"  " real" " 0.1   " 
 Binwidth for the distribution

.BI "\-[no]sham"  "yes   "
 Turn off energy weighting even if energies are given

.BI "\-tsham"  " real" " 298.15" 
 Temperature for single histogram analysis

.BI "\-pmin"  " real" " 0     " 
 Minimum probability. Anything lower than this will be set to zero

.BI "\-dim"  " vector" " 1 1 1" 
 Dimensions for distances, used for volume correction (max 3 values, dimensions  3 will get the same value as the last)

.BI "\-ngrid"  " vector" " 32 32 32" 
 Number of bins for energy landscapes (max 3 values, dimensions  3 will get the same value as the last)

.BI "\-xmin"  " vector" " 0 0 0" 
 Minimum for the axes in energy landscape (see above for  3 dimensions)

.BI "\-xmax"  " vector" " 1 1 1" 
 Maximum for the axes in energy landscape (see above for  3 dimensions)

.BI "\-pmax"  " real" " 0     " 
 Maximum probability in output, default is calculate

.BI "\-gmax"  " real" " 0     " 
 Maximum free energy in output, default is calculate

.BI "\-emin"  " real" " 0     " 
 Minimum enthalpy in output, default is calculate

.BI "\-emax"  " real" " 0     " 
 Maximum enthalpy in output, default is calculate

.BI "\-nlevels"  " int" " 25" 
 Number of levels for energy landscape

.BI "\-mname"  " string" " " 
 Legend label for the custom landscape

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
